Recovery Overview - Dry Years
01/29/24
This document walks through the Reorienting to Recovery’s Recovery Definition and evaluates how the Dry Years Blended Scenario Performs. It provides summary statistics and visualizations to evaluate recovery according to defined thresholds recovery metrics (Threshold Recovery Metrics table below) and to explore results associated with non thereshold biological metrics (Additional Biological Metrics table below).
Review Indicator Populations
The Reorienting to Recovery selected a few indicator populations as a starting point for evaluating recovery of scenarios. For the Fall Run Chinook model, we selected:
Upper Sacramento River
American River (?)
Stanislaus River
Tuolumne River
Indicator rivers must meet all recovery metrics in last 15 years of the simulation.
Secondarily, all independent populations must meet recovery in at least 5 years and the percentage of ind populations that meet recovery objects must be above 80% in last 15 years.
Review Biological Recovery Metrics
Threshold Recovery Metrics
The table below summarizes Recovery Metrics that have associated Recovery Thresholds. For each of these metrics, scenarios are evaluated to see what percentage or tributaries or years they achieve the recovery target for each scenario.
| Value | Performancemeasure | Description | Target/Recovery Threshold |
| 1: Salmonid abundance | 1: Adult abundance | Represents an interest in increasing salmonid abundance across the Central Valley. Can be estimated with models as annual number of adult spawning salmonids in each tributary and ocean, tracked for 20 years. Adult abundance for each year and tributary is a direct output from the SIT DSMs and is summarized to show average Central Valley annual abundance. | 500 or more spawners |
| 2: Salmonid productivity | 2.1: Cohort Replacement | Represents an interest in having growing or stable salmonid populations. CRR can be estimated with models as the adult natural origin return ratio in each tributary, tracked for 20 years. CRR is calculated as the number of natural origin adult returns in year X+3 divided by the number of in-river spawners in year X. CRR is calculated for each year and tributary and then averaged across tributaries and years. | Mean CRR > 1 |
| 2: Salmonid productivity | 2.2: Population growth rate | Represents an alternative way to capture growing or stable salmonid populations. Can be estimated with models as average trend in population growth over a 20-year period. | Mean Growth Rate > 1 |
| 4: Salmonid genetic diversity | 4: pHOS | Represents an interest in preserving genetic diversity of natural populations and minimizing potential negative demographic effects from hatchery origin fish. Salmonid models are currently being modified to estimate proportion of hatchery origin spawners (pHOS). | pHOS < 5% |
Additional Biological Recovery Metrics
The table below provides additional recovery metrics to help balance and refine scenarios. This set of metrics does not have clear threshold values that indicate recovery but instead provides additional context to help select more balanced scenarios.
| Value | Performance measure | Description |
| 3: Salmonid spatial structure | 3.1: Independent populations | Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific abundance estimates from models can be used to calculate the number of independent viable populations in each diversity group per ESU/run. |
| 3: Salmonid spatial structure | 3.2: % of potential independent populations | Represents an alternative way to capture the distribution of salmonid, calculated as the % of potential independent viable populations in each diversity group per ESU/run. |
| 3: Salmonid spatial structure | 3.3: Dependent populations | Represents an interest in increasing and maintaining the distribution of salmonids across historically occupied watersheds. Watershed-specific CV Salmon Recovery abundance estimates from models can be used to calculate the number of dependent populations in each diversity group per ESU/run. |
| 5: Salmonid life history diversity | 5.1: Age distribution of spawning adults | Represents an interest in preserving life history diversity (age of spawners) in natural populations. Salmonid models can be used to estimate the minimum % of each age class of adults and check if targets are met (Age 4 >35%, Age 5+ >20%). |
| 5: Salmonid life history diversity | 5.2: Size distribution of juveniles | Represents an interest in preserving life history diversity (size distribution of juveniles) in natural populations. Salmonid models can be used to estimate the variation in juvenile abundance of each life stage (fry, parr, yearling) and calculate variation across years. Size distribution of juveniles is summarized in a single metric by using a Shannon diversity index. |
| 5: Salmonid life history diversity | 5.3: Size and timing of juveniles at ocean entry | Represents an interest in preserving life history diversity (size and timing of juveniles at ocean entry) in natural populations. Size distribution and timing of juveniles at ocean entry is summarized in a single metric by using a Shannon diversity index. |
| 5: Salmonid life history diversity | 5.4: Habitat diversity | Represents an interest in preserving habitat diversity that facilitates life history diversity in natural populations. Could be estimated as the amount and relative % of available habitat of different types (measured in area and days). Specific methods using the salmon models to calculate and compare optimal habitat ratios to population growth are being developed. |
| 6: Abundance, productivity, and distribution at levels that support ecosystem health | 6: Ecosystem health | Represents an interest in maintaining resilient and functioning ecosystems due to adequate salmonid abundance. Could be captured with a proxy metric of ratio of spawner abundance to habitat (marine derived nutrient proxy). The marine derived nutrient proxy metric gives the grams of marine nutrient per square meters of river. To calculate marine derived nutrient proxy, we calculated the total acres by multiplying habitat extent lengths by river width. We then multiplied the average annual number of spawners by the average weight (assumed 21 grams) and divided by our total area CV Salmon Recovery Draft for Planning Team Review 11 (square meters) to get a grams of marine derived nutrient per square meters. |
| 7: Biological recovery objectives met by certain time | 7: Time to biological recovery | Represents an interest to recover salmonids quickly. Can be estimated by salmon models as the # of years until recovery objectives are met. See Phase 1 report for a list of recovery objectives. |
Review Dry Years Scenario
The Dry Years scenario includes efforts in each of the 4 knobs that we can turn in the R2R process: Habitat, Hydrology, Harvest (oceans & rivers) and Hatcheries. The table below summarizes the Dry Years scenario in comparison to the Baseline scenario.
| Recovery scenario | Habitat | Hydrology | Harvest (oceans & rivers) | Hatcheries |
|---|---|---|---|---|
| Baseline | Current + planned | Current operations | Current levels | Current operations |
| Dry Years | Max habitat, Food subsidies, Predation reduction (Dry Years) | EFF (dry years) | No harvest of dry Cohort | Terminal Hatcheries (current output number) |
Run Dry Years Scenario
The following code block runs the Dry Years scenario.
#TODO discuss leads with tech team - harvest is playing a big role in the big dip - once you allow dry year in there you allow for harvest you only get a small dip and then rise again - Also increasing delta survival gets us above 500 spawners for a consecuative 5 year period everywhere… - The delta + outmigration survival gauntlet seems to be diminishing pops (all but tribs that are less strong get diminished ) - All of the default calibration tribs are starting out the simulation with very few spawners seeds show limited pops on all tribs except main ones
test_seeds <- fallRunDSM::adult_seeds
test_seeds[1] <- rowMeans(DSMCalibrationData::grandtab_imputed$fall)
# Dry Years --
new_params_dy <- fallRunDSM::r_to_r_dry_years_params
new_params_dy$movement_hypo_weights <- c(1, rep(0, 7))
# BASELINE --
new_params <- fallRunDSM::r_to_r_baseline_params
new_params$movement_hypo_weights <- c(1, rep(0, 7))
# seed
r2r_seeds_dy <- fallRunDSM::fall_run_model(mode = "seed",
seeds = fallRunDSM::adult_seeds,
..params = new_params, # seed with baseline, then Dry Years
delta_surv_inflation = FALSE)
# run model
r2r_model_results_dy <- fallRunDSM::fall_run_model(mode = "simulate",
..params = new_params_dy,
seeds = r2r_seeds_dy,
delta_surv_inflation = TRUE)Results
Model results should be evaluated relative to the Baseline model. The following plots show the % difference from baseline results for the Dry Years scenario. You can look at the tab to the right to see the total spawner trends of the Dry Years Scenario in comparison to the Baseline Scenario. (Make add a percent difference table in here too) - Think through the best way to present these. Also add a percent difference bar plot)
% Difference from Baseline (all watersheds)
% Difference from Baseline (all watersheds)
Spawners Plot
Diagnostic Plots
## Rows: 252
## Columns: 6
## $ month <chr> "jan", "jan", "jan", "jan", "jan", "jan", "jan"…
## $ year <chr> "1980", "1981", "1982", "1983", "1984", "1985",…
## $ flows <dbl> 767.0468, 523.8617, 438.7412, 854.6591, 340.708…
## $ date <date> 1980-01-01, 1981-01-01, 1982-01-01, 1983-01-01…
## $ sac_migratory_survival <dbl> 0.508, 0.508, 0.508, 0.508, 0.508, 0.508, 0.189…
## $ outmigration_month <chr> "Outmigration Month", "Outmigration Month", "Ou…
## Rows: 682
## Columns: 4
## $ year <chr> "1979", "1979", "1979", "1979"…
## $ location <chr> "American River", "Antelope Cr…
## $ average_monthly_annual_spawning_habitat <dbl> 960725.353, 60038.788, 1625.00…
## $ spawner_capacity <dbl> 103415, 6463, 175, 4700, 1646,…
## $fall
## 1998 1999 2000 2001 2002 2003 2004 2005
## Upper Sacramento River 6318 161192 96688 75296 65690 89229 43604 57012
## Antelope Creek 72 72 72 72 72 72 72 72
## Battle Creek 53957 92929 53447 100604 397149 64764 23861 20520
## Bear Creek 34 34 34 34 34 34 34 34
## Big Chico Creek 40 40 40 40 40 40 40 40
## Butte Creek 500 1590 1590 4433 3665 3492 2516 4255
## Clear Creek 4259 8003 6687 10865 16071 9475 6365 14824
## Cottonwood Creek 1355 1355 1355 1355 1355 1355 1355 1355
## Cow Creek 1589 1589 1589 1589 1589 1589 1589 1589
## Deer Creek 270 587 587 587 587 587 300 963
## Elder Creek 40 40 40 40 40 40 40 40
## Mill Creek 546 1218 1218 1218 2611 2426 1192 2426
## Paynes Creek 85 85 85 85 85 85 85 85
## Stony Creek 40 40 40 40 40 40 40 40
## Thomes Creek 40 40 40 40 40 40 40 40
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0
## Bear River 40 40 40 40 40 40 40 40
## Feather River 58742 58742 106490 165833 97621 83495 50286 45634
## Yuba River 28860 22492 13920 21714 22326 26285 4837 9106
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0
## American River 50457 55339 100852 135384 124252 163742 99230 62679
## Lower Sacramento River 0 0 0 0 0 0 0 0
## Calaveras River 40 40 40 40 40 40 40 40
## Cosumnes River 300 229 460 531 1350 122 1208 370
## Mokelumne River 4122 2183 1973 2307 2840 2122 1588 10406
## Merced River 3292 3129 11130 9181 8866 2530 3270 1942
## Stanislaus River 3087 4349 8498 7033 7787 5902 4015 1427
## Tuolumne River 8910 8232 17873 8782 7173 2163 1984 668
## San Joaquin River 0 0 0 0 0 0 0 0
## 2006 2007 2008 2009 2010 2011 2012 2013
## Upper Sacramento River 55468 17061 24743 5827 16372 11957 28701 40084
## Antelope Creek 72 72 72 72 72 72 72 72
## Battle Creek 19493 9904 4286 3047 6632 12513 31554 30834
## Bear Creek 34 140 19 6 34 34 34 34
## Big Chico Creek 40 40 40 40 40 40 40 40
## Butte Creek 1920 1225 275 306 370 416 813 2200
## Clear Creek 8422 4157 7677 3228 7192 4841 7631 13337
## Cottonwood Creek 1355 1250 510 1055 1137 2144 2556 2774
## Cow Creek 4209 2044 478 261 536 1810 1488 3011
## Deer Creek 1905 563 194 58 166 662 873 1026
## Elder Creek 40 40 40 40 40 40 40 40
## Mill Creek 1403 851 218 102 144 1231 890 2197
## Paynes Creek 85 85 85 85 85 85 85 175
## Stony Creek 40 40 40 40 40 40 40 40
## Thomes Creek 40 40 40 40 40 40 40 40
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0
## Bear River 40 40 40 40 40 40 40 40
## Feather River 70934 20338 5513 4499 41693 43898 59084 140365
## Yuba River 4029 1007 1236 2770 4163 6794 5450 11181
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0
## American River 24540 10120 2514 5297 14688 25626 38328 58228
## Lower Sacramento River 0 0 0 0 0 0 0 0
## Calaveras River 40 40 40 40 40 40 40 40
## Cosumnes River 530 77 15 531 740 53 1071 531
## Mokelumne River 1732 470 173 680 1920 2674 5471 7071
## Merced River 1429 485 389 358 651 1571 2011 2826
## Stanislaus River 1923 443 865 595 1086 1309 4006 2845
## Tuolumne River 562 224 388 124 540 893 783 1926
## San Joaquin River 0 0 0 0 0 0 0 0
## 2014 2015 2016 2017
## Upper Sacramento River 34876 28660 4291 2149
## Antelope Creek 143 6 138 3
## Battle Creek 27064 3642 1236 354
## Bear Creek 34 2 32 2
## Big Chico Creek 40 40 40 40
## Butte Creek 1412 82 626 105
## Clear Creek 15794 8809 2481 2353
## Cottonwood Creek 1940 604 813 124
## Cow Creek 3535 591 822 288
## Deer Creek 849 612 253 106
## Elder Creek 40 40 40 40
## Mill Creek 2488 1033 602 342
## Paynes Creek 72 85 8 85
## Stony Creek 40 40 40 40
## Thomes Creek 40 40 40 40
## Upper-mid Sacramento River 0 0 0 0
## Sutter Bypass 0 0 0 0
## Bear River 40 40 40 40
## Feather River 56811 19091 35994 9779
## Yuba River 9757 6567 3766 1517
## Lower-mid Sacramento River 0 0 0 0
## Yolo Bypass 0 0 0 0
## American River 26475 15732 14473 9886
## Lower Sacramento River 0 0 0 0
## Calaveras River 40 40 40 40
## Cosumnes River 373 204 1248 670
## Mokelumne River 3297 4581 1984 5639
## Merced River 922 1247 2541 3191
## Stanislaus River 3060 6136 9330 5655
## Tuolumne River 438 113 1347 1096
## San Joaquin River 0 0 0 0
##
## $late_fall
## 1998 1999 2000 2001 2002 2003 2004 2005 2006
## Upper Sacramento River 39340 8683 8702 19276 36004 5494 8824 10524 10163
## Antelope Creek 0 0 0 0 0 0 0 0 0
## Battle Creek 61 61 61 98 216 57 40 23 50
## Bear Creek 0 0 0 0 0 0 0 0 0
## Big Chico Creek 0 0 0 0 0 0 0 0 0
## Butte Creek 0 0 0 0 0 0 0 0 0
## Clear Creek 100 100 100 100 100 110 60 94 42
## Cottonwood Creek 0 0 0 0 0 0 0 0 0
## Cow Creek 0 0 0 0 0 0 0 0 0
## Deer Creek 0 0 0 0 0 0 0 0 0
## Elder Creek 0 0 0 0 0 0 0 0 0
## Mill Creek 0 0 0 0 0 0 0 0 0
## Paynes Creek 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0
## Thomes Creek 0 0 0 0 0 0 0 0 0
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0
## Feather River 0 0 0 0 0 0 0 0 0
## Yuba River 0 0 0 0 0 0 0 0 0
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0
## Calaveras River 0 0 0 0 0 0 0 0 0
## Cosumnes River 0 0 0 0 0 0 0 0 0
## Mokelumne River 0 0 0 0 0 0 0 0 0
## Merced River 0 0 0 0 0 0 0 0 0
## Stanislaus River 0 0 0 0 0 0 0 0 0
## Tuolumne River 0 0 0 0 0 0 0 0 0
## San Joaquin River 0 0 0 0 0 0 0 0 0
## 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
## Upper Sacramento River 15275 3964 3334 4282 3686 2822 5227 7950 2131 3085
## Antelope Creek 0 0 0 0 0 0 0 0 0 0
## Battle Creek 72 19 32 27 28 19 42 120 97 57
## Bear Creek 0 0 0 0 0 0 0 0 0 0
## Big Chico Creek 0 0 0 0 0 0 0 0 0 0
## Butte Creek 0 0 0 0 0 0 0 0 0 0
## Clear Creek 69 55 336 91 58 50 77 72 272 55
## Cottonwood Creek 0 0 0 0 0 0 0 0 0 0
## Cow Creek 0 0 0 0 0 0 0 0 0 0
## Deer Creek 0 0 0 0 0 0 0 0 0 0
## Elder Creek 0 0 0 0 0 0 0 0 0 0
## Mill Creek 0 0 0 0 0 0 0 0 0 0
## Paynes Creek 0 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0 0
## Thomes Creek 0 0 0 0 0 0 0 0 0 0
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0 0
## Feather River 0 0 0 0 0 0 0 0 0 0
## Yuba River 0 0 0 0 0 0 0 0 0 0
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0 0
## Calaveras River 0 0 0 0 0 0 0 0 0 0
## Cosumnes River 0 0 0 0 0 0 0 0 0 0
## Mokelumne River 0 0 0 0 0 0 0 0 0 0
## Merced River 0 0 0 0 0 0 0 0 0 0
## Stanislaus River 0 0 0 0 0 0 0 0 0 0
## Tuolumne River 0 0 0 0 0 0 0 0 0 0
## San Joaquin River 0 0 0 0 0 0 0 0 0 0
## 2017
## Upper Sacramento River 3069
## Antelope Creek 0
## Battle Creek 43
## Bear Creek 0
## Big Chico Creek 0
## Butte Creek 0
## Clear Creek 55
## Cottonwood Creek 0
## Cow Creek 0
## Deer Creek 0
## Elder Creek 0
## Mill Creek 0
## Paynes Creek 0
## Stony Creek 0
## Thomes Creek 0
## Upper-mid Sacramento River 0
## Sutter Bypass 0
## Bear River 0
## Feather River 0
## Yuba River 0
## Lower-mid Sacramento River 0
## Yolo Bypass 0
## American River 0
## Lower Sacramento River 0
## Calaveras River 0
## Cosumnes River 0
## Mokelumne River 0
## Merced River 0
## Stanislaus River 0
## Tuolumne River 0
## San Joaquin River 0
##
## $winter
## 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007
## Upper Sacramento River 2893 3264 1261 8120 7337 8133 7784 15730 17197 2487
## Antelope Creek 0 0 0 0 0 0 0 0 0 0
## Battle Creek 347 391 151 973 879 975 933 1885 2061 298
## Bear Creek 0 0 0 0 0 0 0 0 0 0
## Big Chico Creek 0 0 0 0 0 0 0 0 0 0
## Butte Creek 0 0 0 0 0 0 0 0 0 0
## Clear Creek 0 0 0 0 0 0 0 0 0 0
## Cottonwood Creek 0 0 0 0 0 0 0 0 0 0
## Cow Creek 0 0 0 0 0 0 0 0 0 0
## Deer Creek 0 0 0 0 0 0 0 0 0 0
## Elder Creek 0 0 0 0 0 0 0 0 0 0
## Mill Creek 0 0 0 0 0 0 0 0 0 0
## Paynes Creek 0 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0 0
## Thomes Creek 0 0 0 0 0 0 0 0 0 0
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0 0
## Feather River 0 0 0 0 0 0 0 0 0 0
## Yuba River 0 0 0 0 0 0 0 0 0 0
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0 0
## Calaveras River 0 0 0 0 0 0 0 0 0 0
## Cosumnes River 0 0 0 0 0 0 0 0 0 0
## Mokelumne River 0 0 0 0 0 0 0 0 0 0
## Merced River 0 0 0 0 0 0 0 0 0 0
## Stanislaus River 0 0 0 0 0 0 0 0 0 0
## Tuolumne River 0 0 0 0 0 0 0 0 0 0
## San Joaquin River 0 0 0 0 0 0 0 0 0 0
## 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017
## Upper Sacramento River 2725 4416 1533 738 2578 5920 2627 3182 1409 795
## Antelope Creek 0 0 0 0 0 0 0 0 0 0
## Battle Creek 327 529 184 88 309 709 315 381 169 95
## Bear Creek 0 0 0 0 0 0 0 0 0 0
## Big Chico Creek 0 0 0 0 0 0 0 0 0 0
## Butte Creek 0 0 0 0 0 0 0 0 0 0
## Clear Creek 0 0 0 0 0 0 0 0 0 0
## Cottonwood Creek 0 0 0 0 0 0 0 0 0 0
## Cow Creek 0 0 0 0 0 0 0 0 0 0
## Deer Creek 0 0 0 0 0 0 0 0 0 0
## Elder Creek 0 0 0 0 0 0 0 0 0 0
## Mill Creek 0 0 0 0 0 0 0 0 0 0
## Paynes Creek 0 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0 0
## Thomes Creek 0 0 0 0 0 0 0 0 0 0
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0 0
## Feather River 0 0 0 0 0 0 0 0 0 0
## Yuba River 0 0 0 0 0 0 0 0 0 0
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0 0
## Calaveras River 0 0 0 0 0 0 0 0 0 0
## Cosumnes River 0 0 0 0 0 0 0 0 0 0
## Mokelumne River 0 0 0 0 0 0 0 0 0 0
## Merced River 0 0 0 0 0 0 0 0 0 0
## Stanislaus River 0 0 0 0 0 0 0 0 0 0
## Tuolumne River 0 0 0 0 0 0 0 0 0 0
## San Joaquin River 0 0 0 0 0 0 0 0 0 0
##
## $spring
## 1998 1999 2000 2001 2002 2003 2004 2005 2006
## Upper Sacramento River 1115 262 43 621 195 326 370 30 326
## Antelope Creek 154 40 9 8 46 46 3 82 102
## Battle Creek 178 73 78 111 222 221 90 73 221
## Bear Creek 0 0 0 0 0 0 0 0 0
## Big Chico Creek 369 27 27 39 101 81 101 37 299
## Butte Creek 20259 3679 4118 18670 16409 17404 10558 17592 6537
## Clear Creek 47 35 9 99 66 25 98 69 77
## Cottonwood Creek 477 102 122 245 125 73 17 47 55
## Cow Creek 0 0 0 0 0 0 0 0 0
## Deer Creek 1879 1591 637 1622 2195 2759 804 2239 2432
## Elder Creek 0 0 0 0 0 0 0 0 0
## Mill Creek 424 560 544 1104 1594 1426 998 1150 1002
## Paynes Creek 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0
## Thomes Creek 1 2 2 2 2 2 2 2 2
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0
## Feather River 4538 4538 8227 12812 7542 6451 3885 3526 5480
## Yuba River 2230 1738 1075 1678 1725 2031 1618 5274 1456
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0
## Calaveras River 40 40 40 40 40 40 40 40 40
## Cosumnes River 40 40 40 40 40 40 40 40 40
## Mokelumne River 40 40 40 40 40 40 40 40 40
## Merced River 40 40 40 40 40 40 40 40 40
## Stanislaus River 40 40 40 40 40 40 40 40 40
## Tuolumne River 40 40 40 40 40 40 40 40 40
## San Joaquin River 0 0 0 0 0 0 0 0 0
## 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016
## Upper Sacramento River 248 52 326 326 326 326 326 326 326 326
## Antelope Creek 26 3 32 17 6 1 32 7 5 7
## Battle Creek 291 105 194 172 157 799 608 429 181 180
## Bear Creek 0 0 0 0 0 0 0 0 0 0
## Big Chico Creek 101 101 6 2 124 101 101 101 101 101
## Butte Creek 6871 11046 2687 1991 4871 16317 16782 5083 569 5731
## Clear Creek 194 200 120 21 8 68 659 95 45 29
## Cottonwood Creek 34 88 88 15 2 1 1 2 88 88
## Cow Creek 0 0 0 0 0 0 0 0 0 0
## Deer Creek 644 140 213 262 271 734 708 830 268 331
## Elder Creek 0 0 0 0 0 0 0 0 0 0
## Mill Creek 920 381 220 482 366 768 644 679 127 175
## Paynes Creek 0 0 0 0 0 0 0 0 0 0
## Stony Creek 0 0 0 0 0 0 0 0 0 0
## Thomes Creek 2 2 2 2 2 2 2 2 2 2
## Upper-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Sutter Bypass 0 0 0 0 0 0 0 0 0 0
## Bear River 0 0 0 0 0 0 0 0 0 0
## Feather River 1571 426 348 3221 3391 4565 10844 4389 1475 2781
## Yuba River 353 1320 2616 3737 2360 2289 4046 2021 235 291
## Lower-mid Sacramento River 0 0 0 0 0 0 0 0 0 0
## Yolo Bypass 0 0 0 0 0 0 0 0 0 0
## American River 0 0 0 0 0 0 0 0 0 0
## Lower Sacramento River 0 0 0 0 0 0 0 0 0 0
## Calaveras River 40 40 40 40 40 40 40 40 40 40
## Cosumnes River 40 40 40 40 40 40 40 40 40 40
## Mokelumne River 40 40 40 40 40 40 40 40 40 40
## Merced River 40 40 40 40 40 40 40 40 40 40
## Stanislaus River 40 40 40 40 40 40 40 40 40 40
## Tuolumne River 40 40 40 40 40 40 40 40 40 40
## San Joaquin River 0 0 0 0 0 0 0 0 0 0
## 2017
## Upper Sacramento River 326
## Antelope Creek 8
## Battle Creek 30
## Bear Creek 0
## Big Chico Creek 101
## Butte Creek 565
## Clear Creek 25
## Cottonwood Creek 88
## Cow Creek 0
## Deer Creek 219
## Elder Creek 0
## Mill Creek 258
## Paynes Creek 0
## Stony Creek 0
## Thomes Creek 2
## Upper-mid Sacramento River 0
## Sutter Bypass 0
## Bear River 0
## Feather River 756
## Yuba River 117
## Lower-mid Sacramento River 0
## Yolo Bypass 0
## American River 0
## Lower Sacramento River 0
## Calaveras River 40
## Cosumnes River 40
## Mokelumne River 40
## Merced River 40
## Stanislaus River 40
## Tuolumne River 40
## San Joaquin River 0Threshold Biological Performance Metrics
The two tabs below show plots that describe if a tributary meets the recovery objective.
Abundance and Genetic Diversity metrics are evaluated for each Independent population in every year of the scenario.
Productivity Metrics are averaged for each independent population over the last 10 years of the simulation. Productivity metrics must on average for each independent population, meet recovery thresholds to consider the system at recovery.
(TODO: maybe color indicator pops differently)
Abundance and Genetic Diversity
Productivity Metrics
Additional Biological Performance Metics
Spatial Structure
## Rows: 1,240
## Columns: 12
## $ location <chr> "American River", "American River", "America…
## $ year <dbl> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 1…
## $ scenario <chr> "Dry Years", "Dry Years", "Dry Years", "Dry …
## $ run <chr> "fall", "fall", "fall", "fall", "fall", "fal…
## $ performance_metric <chr> "1 All Spawners", "1 All Spawners", "1 All S…
## $ value <dbl> 105670, 61527, 115575, 203233, 123711, 14130…
## $ origin <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ size_or_age <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ month <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ `Spawners Present` <dbl> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
## $ diversity_group <fct> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,…
## $ div_group_with_watersheds <chr> "5:", "5:", "5:", "5:", "5:", "5:", "5:", "5…## # A tibble: 4 × 1
## location
## <chr>
## 1 Battle Creek
## 2 Bear Creek
## 3 Cow Creek
## 4 Upper Sacramento River